Nucleic Acids Research, 2003, Vol. 31, No. 19 5754-5763
© 2003 Oxford University Press
G-quartets direct assembly of HIV-1 nucleocapsid protein along single-stranded DNA
1 Laboratoire de Microscopie Moléculaire et Cellulaire, CNRS-UMR 8126, Institut Gustave Roussy, 39 rue Camille Desmoulins, 94805 Villejuif, France, 2 AIDS Vaccine Program, SAIC Frederick, Inc., NCI at Frederick, Frederick, MD 21702, USA and 3 Laboratoire de Biophysique, Muséum National d’Histoire Naturelle, USM 0503, INSERM U565, CNRS UMR 8646, 43 rue Cuvier, 75231 cedex 05, Paris, France
*To whom correspondence should be addressed. Tel: +33 1 42114880; Fax: +33 1 42115494; Email: mirambe{at}igr.fr
The d(TTGGGGGGTACAGTGCA) sequence, derived from the human immunodeficiency virus type 1 (HIV-1) central DNA flap, can form in vitro an intermolecular parallel DNA quadruplex. This work demonstrates that the HIV-1 nucleocapsid protein (NCp) exhibits a high affinity (108 M–1) for this quadruplex. This interaction is predominantly hydrophobic, maintained by a stabilization between G-quartet planes and the C-terminal zinc finger of the protein. It also requires 5 nt long tails flanking the quartets plus both the second zinc-finger and the N-terminal domain of NCp. The initial binding nucleates an ordered arrangement of consecutive NCp along the four single-stranded tails. Such a process requires the N-terminal zinc finger, and was found to occur for DNA site sizes shorter than usual in a sequence-dependent manner. Concurrently, NCp binding is efficient on a G'2 quadruplex also derived from the HIV-1 central DNA flap. Apart from their implication within the DNA flap, these data lead to a model for the nucleic acid architecture within the viral nucleocapsid, where adjacent single-stranded tails and NCp promote a compact assembly of NCp and nucleic acid growing from stably and primary bound NCp.
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